Penance Paid
by SioraiDragon
Summary: The Doctor had been running for so long, after all of his mistakes. Especially after the disaster on Mars. So his enemies trap him within an inescapable prison, attempting to have him pay for the suffering of the universe. So when his friends discover him after centuries of solitude, can they save him from the one person who hates him the most?
1. A Lack of Thoughts in the Dark

It was so quiet in here now. Even the constant barrage of thoughts had dimmed some time ago. The black was all encompassing, feeling long forgotten. He's not even sure if his fingers exist anymore. If they did, they were as lifeless as he was. His hair a bit longer, still all sticky-uppy, but he thought it was only because of the regenerative field that kept him his youthful guise.

A hollow feeling in his chest, heavy and almost drowning him in nothing. He wanted something, anything to stop the hollowness. He begged and pleaded. _Someone please. I'll do anything. Please let me out please._

Usually his enemies would answer. They'd try to kill him. And he'd welcome that. He'd even thank them. Just please, _let him out_.

It occurs to him, in the passing of the rare thoughts, would he be able to see again? His eyes have been in the dark for what feels like centuries. Animals born and raised in dark, cave-like environments always went blind in their lifetime. After all, other than the nightmares, he hasn't seen anything other than the inky dark. It was maddening on his senses, his hearing so sharp he felt he could hear his blood being pumped to his toes.

To make matters worse, the moments trickled by, so painfully slow, as if each microsecond was stretched out to an hour. The familiar turn of the planet spinning was making him nauseous. He hated it, loathed that this place was trying so hard to train him to never run again. To be pliant and obedient, to tame the Oncoming Storm. What was worse was that he was slowly starting to comply.

He had tried to fight it for so long. It was who he was, what he'd been doing for so long. His wanderlust had kept him so tied to his morals.

But after he thought about his love for running through time and space, he began to feel the coolness of something slipping into his blood stream. He didn't know what specifically they were for. The needles had ingrained themselves into his wrists since his first hour had passed in the prison.

The dull ache came when he expected it to. These weren't the nutrient tubes or the hydration drips. The nightmares were coming again. It wasn't subtle, something constant and painful whenever it was used. A drug from some foreign planet it hurt to try and think of the name of. He started to panic as lucidity was beginning to slip away again, and he was just left in a state where a single thought couldn't enter his head. He gripped the armrest, manacles tightening against his arms to ensure he doesn't try and hurt himself or yank out the drug line. He's tried so many times to resist that he felt the manacles dig into his hands and something start to compress his chest that he had to rely on his respiratory bypass to keep him somewhat awake. His head felt like it was stuffed with lead and if he even thought about moving it sent his head into a spin.

His wardens had made him see so many of his failures. So many faces of those he failed to save. Their haunting eyes, begging for something he could never give them. _I tried. Oh good Rassilon I wanted to save all of you. You all deserve so much better._

And then there was Adelaide.

Her eyes scared him the most. Her gaze of pure disgust that made him feel ever the failure of a Time Lord that everyone expected him to be. He broke the sacred rules of time. He warped them and laughed as he spit on the very essence that kept the universe stable. All because he was just so tired of losing. Tired of rules and delegations and pride that stopped him from saving all of those people. All of those people ( _wonderful, stupid, brilliant people_ ) that had marred his sleep and he spared no day without thinking of them. It was because of them that he always was counting his limited blessings on his fingers and his failures that were just as endless as time. He just wanted to save someone for once, a day where everybody lived. _Could he not have one more day like that?_ But his hearts had finally said enough, and he impulsively just began to fight all of that he was taught to obey. And of course it had to be on the _bloody_ Bowie Base One. _Of bloody course_.

And it proved to be his worst mistake since The Moment.

The eyes were back, staring and searching for a man that no longer existed. Or maybe never existed at all. All that was left was what he himself was beginning to acknowledge as unquestionable truth. About what he was.

A Monster. A Warrior. A Killer. A Coward.

Never a Doctor.

And with that knowledge, he screamed as once more the Pandorica subjected him to his darkest fears.

* * *

Outside, a dusty TARDIS mourned that she couldn't protect her Thief. Her precious pilot. His telepathic connection to Her was severed. He was completely cut off from Her, and She could hear his thoughts. The screams, the swears, the despair.

She had never heard him so hollow.

The TARDIS tried for so long to send messages to his Strays, the ones he brought along and taught and changed the world. But something kept stopping her, enough to the point she almost activated one of the protocols to teleport her out of Stonehenge in order to send it. But She could never leave her beloved Thief. Until she found a crack in the fields surrounding Stonehenge, the ones keeping her messages from sending. A crack, worn away by the centuries spent here in the dark. She reached for it, desperately, throwing her own power into it, so similar to what her Thief did for her in the parallel world to give her life back.

She sent it through her keys, to any electronic able to receive it nearby. just a few words, a single message to as many connected to this Thief as possible.

 _Beneath Stonehenge, help_ _me_.

Timelines shifted and changed but She didn't care. What She hadn't realized was which keys got the message, including ones that shouldn't be possible.

* * *

 **First story written in such a long time! I've missed it and I hope you all enjoy it!**

 **Dragon Out!**


	2. Deep Down Dark Deep Down

**Thanks all for the wonderful reaction to the first chapter! I hope you all enjoy this next one!**

Jack Harkness woke up late, for once. Being in several wars, drafted six times, and then in labor camps for awhile had always trained him to be up a little before sunrise. But at least now he'd had a reason to doze and dream.

Beside him lay his wonderful Ianto, sleeping curled up and still holding onto Jack like a lifeline. He looked years younger, but still old enough to send Jack's heart into a nosedive. His short dark hair was as fluffed up as it could, reminding Jack of a disgruntled puppy. Ianto's intensity was nowhere to be seen, leaving in its wake a smaller, more innocent man. Even Lisa's demise hadn't haunted Jack's lover in a while, and Jack had thought that perhaps finally, Ianto was slowly recovering from the loss.

Jack himself had loved so many before, still harboring feelings for the Doctor who saved him, or sweet Rosie. But Ianto was different, someone who was distant with so many, but so passionate with him. So Jack had began to fall, headfirst, into a love that was starting to scare him. He would outlive Ianto by centuries, and Jack didn't want Ianto to become just a mayfly or a whisper in the story of Jack's life. The captain had resolved then to be the best boyfriend he could be, taking the slow, personal route, all for the sake of Ianto Jones.

The immortal man gently kissed the space between his lover's brows and disentangled their limbs, pulling on his trousers to make some bacon and coffee. He stretched as the pot began to heat, his tired mind still waking up slowly. As he went searching for a pan, he'd heard a muffled groan and looked up to see Ianto shuffling into the kitchen, sleep still in his eyes.

"Your phone woke me up Jackass." Ianto quipped, all in good sarcastic fun. Jack sighed, probably Gwen about to get on his case for not calling in late. Jack rolled his eyes as he swept to the side, grinning in that way that would make so many (hopefully one day his Ianto) sway.

"I'll take care of it love. Start the bacon? Coffee's already done."

Ianto sighed and took Jack's place searching in cabinets. The immortal whistled at the lovely view of a nice rear bumper, with Ianto responding by swearing and threatening to chuck the kettle at him. Jack laughed as he walked to the bedroom, his phone by the rest of his clothes on the floor. He picked it up, a feeling of worry sparking when he saw that it wasn't Gwen. He swallowed, and immediately began searching for his TARDIS key.

The new Doctor he met had given it to him after they met in Utopia, always promising to come back if Jack wanted to see him. Of course Jack had visited the TARDIS since then, on a quick adventure to satisfy his own lust to wander. But the Doctor made him promise to use the key if anything felt like it was too big for the new Torchwood to handle. So far, barring the 456 episode, the captain had found no issue that was major enough to distract his Time Lord friend from his travels across time and space.

He found it still on the simple rope wristlet he'd tied it to, but as soon as he picked it up, it began to singe his fingers. Dropping the hot metal immediately, Jack quickly unlocked his phone to see a text from an unknown number, with a little blue box at the end of the contact name. One message came through.

 _Beneath Stonehenge, help me._

Jack's eyes widened as he felt the worry explode. Soon he was crashing about the room, gathering his trusty WW2 coat and the Vortex Manipulator, and after some hesitation, the same pistol he had when he first met the Doctor. He grabbed the key and tied it to his wrist, and ran down the stairs.

"What in the bloody..."

"Ianto, we gotta go. Get your stuff. We gotta get to the Hub, call Gwen. It's priority mauve."

Ianto's eyes widened, he nodded and ran upstairs. In less than three minutes he looked ready to run. The younger man raised an eyebrow, which Jack recognized as Ianto's "If you don't tell me later, I'll shoot you" eyebrows. If it weren't such an emergency, Jack would be begging to pick up where last night left off. But the immortal resolved to answering questions on the way to Torchwood.

"A Doctor emergency. He's called for help. He's never done that. Not to us specifically. And we need all the help we can get from the team. I'm only bringing those I trust."

Ianto had only seen when Jack's eyes were so concerned a few times. One was the 456 incident. He'd nodded and ran to the car, snatching the keys as he knew Jack would want to drive. Jack ran out, swiftly nabbing the keys and almost left skid marks from how fast he turned the vehicle out of the driveway.

 _We're coming Doc, hold on_

* * *

 _Dreams danced, and stars died. His mind lay scattered in the dust, among the fragments of his sanity. His chest was tight, no matter what superior biology he'd once bragged about coming into play. Was the Pandorica still compressing his chest? The Doctor couldn't even tell anymore._

 _He felt so tired. He just wanted to sleep. Why wouldn't they let him sleep? He wasn't bad anymore, cross both of his hearts!_

 _What more could he promise to? What else did he believe in that meant a lot to him? Everything else was taken, what was left?!_

 _Memories of those long past swirled again, having eyes of judgement on him as he begged, pleaded with them for a respite. He tried, oh Rassilon and Omega above he tried! His friends, his wonderful friends, they'd stay with him. They promised._

 _He was so alone._

" _You have the biggest family on Earth."_

 _The Doctor laughed, bitterly, sadly. Tears were unrestrained, pride one of the first things stripped away once the Pandorica locked. A face passed by, kind eyes, a life ruined because he'd let her in. Sweet Sarah Jane. So full of lies. She told him_ _ **lies**_ _._

 _No one wanted him. They all left. Even the one companion he had after everyone had left him. He'd thought the TARDIS would be there for him, her song in his head, singing the nightmares away as best She could. But apparently, she was tired of him too. Tired of the one who ended her race, a triple genocide in that Moment._

 _The Doctor whimpered, the coolness slipping in once again as he drifted, mind numbing again. Eyes, judging eyes. His own people, cloaks once brilliant with ruby and gold stained maroon and crimson. Half regenerated faces and the children. So many children, so small._

 _His mother._

 _He cried, begging for forgiveness. He had no choice! Everywhere was burning, he could save the universe, but lose her._

 _No. No, that wasn't right. Those words weren't for his home planet. Not even for the one being from that planet that gave a damn about him._

 _No._

 _That was someone else. Someone he'd loved. He lost her. Like everything else was, in the dust._

 _Before he slipped again into the Howling, he remembered something he could believe in._

" _Rose…"_

* * *

A gathering of faces in the dark, below one of the oldest unknowns in human history. So many people, almost a conglomeration of those that had wormed their way into the hearts of an alien man who'd saved them. They had seen the blue box, dusty and worn.

"He wouldn't stay here this long." Mickey Smith muttered as he hefted a large anti-Dalek rifle he'd kept, a souvenir from the time on the Crucible. As much as they'd gotten on each other's nerves when they'd traveled, Mickey and the Doctor had become at least good friends, due to Mickey finally standing up for humanity, and the Doctor knowing he'd been trying.

"A TARDIS wouldn't be this dusty, especially his." Sarah Jane replied, her older eyes furrowing in worry as she clutched at Luke, Sky and their friends. She had planned to go alone until her adopted children demanded they save the man who meant so much to her.

Ianto and Mickey surrounded the TARDIS, backs against her as they almost dared something to emerge from the Doctor's home. Meanwhile, the rest of Torchwood along with Sarah and Martha investigating the large cube beside the blue box.

"What do you think it is?" Gwen asked, her equipment still scanning the runes etched into the mysterious object.

"Some kind of ship? Isomorphic locks? Wouldn't be the first time." Martha muttered as she typed away on a report to UNIT, telling the Brigadier where she and Mickey would be. This felt wrong. Something was wrong, and they were all missing it, she knew it.

"Why don't we open her up then? And if it has answers as to what happened to the Doc, great. If not, we'll blast it sky high." Jack pulled his pistol out, along with the sonic blaster. He stole a glance at Ianto, gesturing for him to stand by him.

"And what if it's deadly?" Sarah Jane huddled her kids together, glaring at the captain as she prepared to rush the young ones into the TARDIS if need be.

"I'll take care of it."

With that he swiftly dialed up the settings on his sonic blaster to encompass the entire front of the mystery cube. The Children of Time swiftly drifted behind Jack as the box hissed and glowed blue-green. Doors slowly drew back with a puff of smoke. With a ding, Gwen glanced down at the translator she'd been running for the script on the sides. She read it out without hesitation.

"This is the Pandorica, the great prison. Here holds the most dangerous monster produced in the multiverse, kept in penance until it paid its price for the suffering of the entirety of time."

Guns raised, the smoke finally dissipated into the air. A collective exhale of horror, the figure they'd recognize anywhere made itself known. But his skin was pale, paler than usual. Brown hair flopped as his head lolled to the side, and he seemed to be swimming in his normally skinny suit. Wires and tubes trailed from his head and hands, and his cuffs were stained copper with old blood.

It was surprisingly Luke who broke the silent spell first. He rushed forward, ignoring his mother's cries of horror. He ran up to the man that had saved his life multiple times and began ripping the wires from his temples. Identic memory served its purpose as he slowly began to disconnect the IVs and tubes from the Time Lord, wanting so badly to have found knowledge on how to help the kind alien.

The young boy heard other noises as his friends began to assist him by trying to find mechanisms to release the myriad of restraints, proving fruitless until his little sister had used her remaining technological powers to open the cuffs, as well as a previously hidden chest restraint.

With nothing holding him anymore, the Doctor began to fall forward, landing in the arms of one Jack Harkness who had appeared out of nowhere. He began to lay the Doctor on the ground, flat as he could, as he felt for his pulse and used limited field medic knowledge to check for injuries.

"The one time you fall into my arms Doc, and I already am going steady with someone." Jack joked, out of habit, even as his eyes began stinging. Almost like a trigger to him, the Doc's eyes snapped open and he leapt up, scrambling away from the crowd amassing him. Fear blocked any noise as he tried to stand, his legs refusing to work as he leapt to the other side of the cave where the Pandorica lay. His eyes were wild and unfocused, fear keeping them dilated and blown out.

"You…you let me out…" The Doctor was quiet, afraid even. He started to shake, and he immediately retched. The senses that had dulled for millennia rushed back, giving his dulled head a migraine. He gripped the walls with fever, determined to try and stand on uncertain legs.

"Why?... I'm a monster… I can hurt you! Why'd you let me out?!" The Doctor cried as he slipped down again, heaving sobs as he breathed his first air in over two thousand years. Torrents of eyes blinked at him as he screamed, at his friends. He'd hurt them again.

Jack glanced to Martha, who already had darted to the medical kit she'd packed from UNIT. She readied a hypodermic, testing the needle as she glanced at her immortal friend. The medical doctor had already drilled the Brigadier for medical records for the Doctor, knowing she'd probably need it. She just wished it wasn't for this.

Jack nodded as he approached his Time Lord friend, gripping him in a strong embrace from behind, to try and dull his screams. If anything, they got worse as soon as he was touched.

"LET ME GO! LET ME GO! I'LL DO ANYTHING, PLEASE! I'M SORRY." The Doctor cried as he struggled, tears flowing as he tried to claw his way out. Don't put him back! He won't run anymore! Don't put him back in the box!

"Shhh… Doc, you're okay… you're free…" Jack mumbled into the Time Lord's too bony shoulder, holding him as tightly as he could. He couldn't let go. He wouldn't. The Doctor needed him, even as he felt the centuries old time traveler's tears wet his shirt.

"I just want to sleep… w-why can't t-they l-l-let me sleep? I-I said I-I was s-s- _sorry_ but I'm still a m-monster." The heaving sobs from the too weary man were deafening and quiet. The utter brokenness from him stunned his Children of Time, who couldn't bare to see their friend in such a way. Martha drifted over, softly gripping a wrist from the Time Lord, and swiftly depositing the sedative into his blood stream.

The cries started again as the Doctor felt the prick of the needle. He didn't want to see the eyes again. Please…

"You're going to sleep Doc, I promise. Just breathe with me."

The Doctor couldn't hear him, his mind going fuzzy. Terrified, he clutched at Jack as he sobs started to quiet unintentionally, eventually falling into a soft whimper as unconsciousness dragged the Time Lord down, for once, without the voices or the eyes. Dreamless and quiet.

 **Just remember folks, these aren't the last of the companions, these are just the ones who are easiest to get to ;)**

 **Dragon Out!**


End file.
